Make GoslingWidget an anywidget

.github/workflows/ci.yml

@@ -14,6 +14,7 @@ concurrency:
 env:
   PYTHONUNBUFFERED: "1"
   FORCE_COLOR: "1"
+  SKIP_DENO_BUILD: "1"
 
 jobs:
 

.github/workflows/docs.yml

@@ -14,6 +14,9 @@ concurrency:
   group: "pages"
   cancel-in-progress: true
 
+env:
+  SKIP_DENO_BUILD: "1"
+
 jobs:
 
   Deploy:

.github/workflows/release.yml

@@ -20,6 +20,9 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+      - uses: denoland/setup-deno@v1
+        with:
+          deno-version: v2.x
       - uses: astral-sh/setup-uv@v3
         with:
           version: "0.5.x"

.gitignore

@@ -16,3 +16,4 @@ node_modules/
 _build/
 generated/
 gallery/
+gosling/static/

deno.json

@@ -0,0 +1,20 @@
+{
+	"lock": false,
+	"nodeModulesDir": "auto",
+	"tasks": {
+		"dev": "deno run -A --node-modules-dir npm:esbuild --bundle --minify --loader:.css=text --format=esm --outfile=gosling/static/widget.js frontend/widget.ts --sourcemap=inline --watch",
+		"build": "deno run -A --node-modules-dir npm:esbuild --bundle --minify --loader:.css=text --format=esm --outfile=gosling/static/widget.js frontend/widget.ts"
+	},
+	"imports": {
+		"@anywidget/types": "npm:@anywidget/types@^0.2.0",
+		"gosling.js": "npm:gosling.js@^0.17.0"
+	},
+	"fmt": {
+		"useTabs": true
+	},
+	"lint": {
+		"rules": {
+			"exclude": ["prefer-const"]
+		}
+	}
+}

frontend/widget.ts

@@ -0,0 +1,23 @@
+import * as gosling from "gosling.js";
+
+interface Model {
+  _viewconf: string;
+}
+
+export default {
+  async render({ model, el }: import("@anywidget/types").RenderProps<Model>) {
+    const viewconf = JSON.parse(model.get("_viewconf"));
+    const api = await gosling.embed(el, viewconf, { padding: 0 });
+    model.on("msg:custom", (msg) => {
+      msg = JSON.parse(msg);
+      console.log(msg);
+      try {
+        const [fn, ...args] = msg;
+        // @ts-expect-error - This is a dynamic call
+        api[fn](...args);
+      } catch (e) {
+        console.error(e);
+      }
+    });
+  },
+};

gosling/_widget.py

@@ -0,0 +1,27 @@
+import json
+import pathlib
+from typing import Any, Dict
+import warnings
+
+import anywidget
+import traitlets as t
+
+_esm = pathlib.Path(__file__).parent / "static" / "widget.js"
+
+if not _esm.exists():
+    warnings.warn("Widget front-end code not found. Assuming running in CI.")
+    _esm = None
+
+
+class GoslingWidget(anywidget.AnyWidget):
+    _esm = _esm
+    _viewconf = t.Unicode("null").tag(sync=True)
+
+    location = t.List(t.Union([t.Float(), t.Tuple()]), read_only=True).tag(sync=True)
+
+    def __init__(self, viewconf: Dict[str, Any], **kwargs):
+        super().__init__(_viewconf=json.dumps(viewconf), **kwargs)
+
+    def zoom_to(self, view_id: str, pos: str, padding: float = 0, duration: int = 1000):
+        msg = json.dumps(["zoomTo", view_id, pos, padding, duration])
+        self.send(msg)

gosling/api.py

@@ -218,7 +218,7 @@ def save(
 
     def widget(self):
         try:
-            from gosling_widget import GoslingWidget
+            from ._widget import GoslingWidget
         except ImportError:
             raise ImportError(
                 "The 'gosling-widget' package is required to use the widget() method."

notebooks/example.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "2a014a14-3d7c-4288-8534-df01d7bf2432",
    "metadata": {},
    "outputs": [],
@@ -12,57 +12,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "61233841",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "Track({\n",
-       "  color: Color({\n",
-       "    shorthand: 's1:N'\n",
-       "  }),\n",
-       "  data: {'type': 'csv', 'url': 'https://raw.githubusercontent.com/sehilyi/gemini-datasets/master/data/circos-segdup-edited.txt', 'chromosomeField': 'c2', 'genomicFields': ['s1', 'e1', 's2', 'e2']},\n",
-       "  height: 130,\n",
-       "  mark: 'withinLink',\n",
-       "  opacity: OpacityValue({\n",
-       "    value: 0.2\n",
-       "  }),\n",
-       "  stroke: StrokeValue({\n",
-       "    value: 'black'\n",
-       "  }),\n",
-       "  strokeWidth: StrokeWidthValue({\n",
-       "    value: 0.5\n",
-       "  }),\n",
-       "  width: 600,\n",
-       "  x: X({\n",
-       "    domain: GenomicDomain({\n",
-       "      chromosome: '1',\n",
-       "      interval: [103900000, 104100000]\n",
-       "    }),\n",
-       "    shorthand: 's1:G'\n",
-       "  }),\n",
-       "  x1: X1({\n",
-       "    domain: GenomicDomain({\n",
-       "      chromosome: '1'\n",
-       "    }),\n",
-       "    shorthand: 's2:G'\n",
-       "  }),\n",
-       "  x1e: X1e({\n",
-       "    shorthand: 'e2:G'\n",
-       "  }),\n",
-       "  xe: Xe({\n",
-       "    shorthand: 'e1:G'\n",
-       "  })\n",
-       "})"
-      ]
-     },
-     "execution_count": 2,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "csvData = gos.csv(\n",
     "    url=\"https://raw.githubusercontent.com/sehilyi/gemini-datasets/master/data/circos-segdup-edited.txt\",\n",
@@ -87,141 +40,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "88f3a522",
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "\n",
-       "<!DOCTYPE html>\n",
-       "<html>\n",
-       "<head>\n",
-       "  <style>.error { color: red; }</style>\n",
-       "  <link rel=\"stylesheet\" href=\"https://unpkg.com/higlass@1.11/dist/hglib.css\">\n",
-       "</head>\n",
-       "<body>\n",
-       "  <div id=\"jupyter-gosling-b21fb3e30816413d991b4879dae37703\"></div>\n",
-       "  <script type=\"module\">\n",
-       "\n",
-       "    async function loadScript(src) {\n",
-       "        return new Promise(resolve => {\n",
-       "            const script = document.createElement('script');\n",
-       "            script.onload = resolve;\n",
-       "            script.src = src;\n",
-       "            script.async = false;\n",
-       "            document.head.appendChild(script);\n",
-       "        });\n",
-       "    }\n",
-       "\n",
-       "    async function loadGosling() {\n",
-       "        // Manually load scripts from window namespace since requirejs might not be\n",
-       "        // available in all browser environments.\n",
-       "        // https://github.com/DanielHreben/requirejs-toggle\n",
-       "        if (!window.gosling) {\n",
-       "            window.__requirejsToggleBackup = {\n",
-       "                define: window.define,\n",
-       "                require: window.require,\n",
-       "                requirejs: window.requirejs,\n",
-       "            };\n",
-       "            for (const field of Object.keys(window.__requirejsToggleBackup)) {\n",
-       "                window[field] = undefined;\n",
-       "            }\n",
-       "\n",
-       "            // load dependencies sequentially\n",
-       "            const sources = [\n",
-       "                \"https://unpkg.com/react@17/umd/react.production.min.js\",\n",
-       "                \"https://unpkg.com/react-dom@17/umd/react-dom.production.min.js\",\n",
-       "                \"https://unpkg.com/pixi.js@6/dist/browser/pixi.min.js\",\n",
-       "                \"https://unpkg.com/gosling.js@0.9.4/dist/gosling.js\",\n",
-       "            ];\n",
-       "\n",
-       "            for (const src of sources) await loadScript(src);\n",
-       "\n",
-       "            // restore requirejs after scripts have loaded\n",
-       "            Object.assign(window, window.__requirejsToggleBackup);\n",
-       "            delete window.__requirejsToggleBackup;\n",
-       "        }\n",
-       "        return window.gosling;\n",
-       "    };\n",
-       "\n",
-       "    var el = document.getElementById('jupyter-gosling-b21fb3e30816413d991b4879dae37703');\n",
-       "    var spec = {\"tracks\": [{\"data\": {\"type\": \"csv\", \"url\": \"https://raw.githubusercontent.com/sehilyi/gemini-datasets/master/data/circos-segdup-edited.txt\", \"chromosomeField\": \"c2\", \"genomicFields\": [\"s1\", \"e1\", \"s2\", \"e2\"]}, \"height\": 130, \"mark\": \"withinLink\", \"width\": 600, \"color\": {\"field\": \"s1\", \"type\": \"nominal\"}, \"opacity\": {\"value\": 0.2}, \"stroke\": {\"value\": \"black\"}, \"strokeWidth\": {\"value\": 0.5}, \"x\": {\"domain\": {\"chromosome\": \"1\", \"interval\": [103900000, 104100000]}, \"field\": \"s1\", \"type\": \"genomic\"}, \"x1\": {\"domain\": {\"chromosome\": \"1\"}, \"field\": \"s2\", \"type\": \"genomic\"}, \"x1e\": {\"field\": \"e2\", \"type\": \"genomic\"}, \"xe\": {\"field\": \"e1\", \"type\": \"genomic\"}}], \"title\": \"Basic Marks: Bar\", \"subtitle\": \"Tutorial Examples\"};\n",
-       "    var opt = {\"padding\": 0, \"theme\": null};\n",
-       "\n",
-       "    loadGosling()\n",
-       "        .then(gosling => gosling.embed(el, spec, opt))\n",
-       "        .catch(err => {\n",
-       "            el.innerHTML = `<div class=\"error\">\n",
-       "    <p>JavaScript Error: ${error.message}</p>\n",
-       "    <p>This usually means there's a typo in your Gosling specification. See the javascript console for the full traceback.</p>\n",
-       "</div>`;\n",
-       "            throw error;\n",
-       "        });\n",
-       "  </script>\n",
-       "</body>\n",
-       "</html>"
-      ],
-      "text/plain": [
-       "View({\n",
-       "  subtitle: 'Tutorial Examples',\n",
-       "  title: 'Basic Marks: Bar',\n",
-       "  tracks: [Track({\n",
-       "    color: Color({\n",
-       "      field: 's1',\n",
-       "      type: 'nominal'\n",
-       "    }),\n",
-       "    data: {'type': 'csv', 'url': 'https://raw.githubusercontent.com/sehilyi/gemini-datasets/master/data/circos-segdup-edited.txt', 'chromosomeField': 'c2', 'genomicFields': ['s1', 'e1', 's2', 'e2']},\n",
-       "    height: 130,\n",
-       "    mark: 'withinLink',\n",
-       "    opacity: OpacityValue({\n",
-       "      value: 0.2\n",
-       "    }),\n",
-       "    stroke: StrokeValue({\n",
-       "      value: 'black'\n",
-       "    }),\n",
-       "    strokeWidth: StrokeWidthValue({\n",
-       "      value: 0.5\n",
-       "    }),\n",
-       "    width: 600,\n",
-       "    x: X({\n",
-       "      domain: GenomicDomain({\n",
-       "        chromosome: '1',\n",
-       "        interval: [103900000, 104100000]\n",
-       "      }),\n",
-       "      field: 's1',\n",
-       "      type: 'genomic'\n",
-       "    }),\n",
-       "    x1: X1({\n",
-       "      domain: GenomicDomain({\n",
-       "        chromosome: '1'\n",
-       "      }),\n",
-       "      field: 's2',\n",
-       "      type: 'genomic'\n",
-       "    }),\n",
-       "    x1e: X1e({\n",
-       "      field: 'e2',\n",
-       "      type: 'genomic'\n",
-       "    }),\n",
-       "    xe: Xe({\n",
-       "      field: 'e1',\n",
-       "      type: 'genomic'\n",
-       "    })\n",
-       "  })]\n",
-       "})"
-      ]
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# just render a view (not a mutable object)\n",
-    "track.view(title=\"Basic Marks: Bar\", subtitle=\"Tutorial Examples\")"
+    "view = track.view(title=\"Basic Marks: Bar\", subtitle=\"Tutorial Examples\", id=\"aa\")\n",
+    "w = view.widget()\n",
+    "w"
    ]
   },
   {
@@ -230,6 +57,16 @@
    "id": "7a82cfcc",
    "metadata": {},
    "outputs": [],
+   "source": [
+    "view.id"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "05d7ecf9-d336-4daa-8d49-447d062f7236",
+   "metadata": {},
+   "outputs": [],
    "source": []
   }
  ],
@@ -249,7 +86,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,